Starting phenix.real_space_refine on Sat Jul 4 21:29:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwp_23553/07_2026/7lwp_23553.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 15004 2.51 5 N 3871 2.21 5 O 4523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23499 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7699 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7697 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7669 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.55, per 1000 atoms: 0.24 Number of scatterers: 23499 At special positions: 0 Unit cell: (128.28, 134.694, 196.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 4523 8.00 N 3871 7.00 C 15004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 26.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.898A pdb=" N GLY A 142 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.986A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.645A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.644A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.845A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 935 through 940 removed outlier: 3.917A pdb=" N LEU A 938 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.762A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.560A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.333A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.672A pdb=" N VAL B 143 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.529A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.508A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.531A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.812A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.592A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.762A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.907A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.586A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.862A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.506A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.709A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.513A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.738A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.548A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.531A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.656A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1033 removed outlier: 4.009A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.444A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.078A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.759A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.396A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.202A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.137A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.797A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.672A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 728 removed outlier: 6.003A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.599A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.672A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.172A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.452A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.389A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN B 564 " --> pdb=" O ARG B 577 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 45 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 565 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.762A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.008A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.323A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.503A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 712 removed outlier: 3.561A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.008A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.933A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 10.065A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 51 removed outlier: 4.012A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.903A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.381A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.942A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.620A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.447A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.447A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.769A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1001 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6338 1.33 - 1.46: 4384 1.46 - 1.58: 13162 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24009 Sorted by residual: bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.59e+01 bond pdb=" C5 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.34e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C5 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 24004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 24727 2.08 - 4.16: 7242 4.16 - 6.24: 648 6.24 - 8.31: 55 8.31 - 10.39: 4 Bond angle restraints: 32676 Sorted by residual: angle pdb=" CA PHE B 515 " pdb=" CB PHE B 515 " pdb=" CG PHE B 515 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" CA PHE B 400 " pdb=" CB PHE B 400 " pdb=" CG PHE B 400 " ideal model delta sigma weight residual 113.80 120.09 -6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.31e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 ... (remaining 32671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13018 17.95 - 35.89: 762 35.89 - 53.84: 142 53.84 - 71.78: 51 71.78 - 89.72: 37 Dihedral angle restraints: 14010 sinusoidal: 5349 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.27 75.27 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 151.38 -58.38 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA THR C 599 " pdb=" C THR C 599 " pdb=" N PRO C 600 " pdb=" CA PRO C 600 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2621 0.095 - 0.190: 1064 0.190 - 0.285: 139 0.285 - 0.379: 19 0.379 - 0.474: 5 Chirality restraints: 3848 Sorted by residual: chirality pdb=" CA LEU A 878 " pdb=" N LEU A 878 " pdb=" C LEU A 878 " pdb=" CB LEU A 878 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA GLN A 784 " pdb=" N GLN A 784 " pdb=" C GLN A 784 " pdb=" CB GLN A 784 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA LEU B1034 " pdb=" N LEU B1034 " pdb=" C LEU B1034 " pdb=" CB LEU B1034 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 3845 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.344 2.00e-02 2.50e+03 1.84e-01 8.51e+02 pdb=" CG TRP C 886 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.178 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.129 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.270 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.201 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.064 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " -0.130 2.00e-02 2.50e+03 1.40e-01 2.44e+02 pdb=" CG ASN C1074 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " 0.218 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.123 2.00e-02 2.50e+03 1.40e-01 2.43e+02 pdb=" CG ASN B1074 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.167 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 10839 2.98 - 3.46: 22215 3.46 - 3.94: 38901 3.94 - 4.42: 42895 4.42 - 4.90: 73319 Nonbonded interactions: 188169 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.498 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.521 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.522 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.522 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.523 3.040 ... (remaining 188164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 241 or (resi \ d 242 through 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 280 or (resid 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 479 or (resid 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N or \ name CA or name C or name O or name CB )) or resid 489 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 747 or (resid 748 and (name N or name CA or name C or n \ ame O or name CB )) or resid 749 through 810 or (resid 811 and (name N or name C \ A or name C or name O or name CB )) or resid 813 through 827 or resid 855 throug \ h 866 or (resid 867 through 868 and (name N or name CA or name C or name O or na \ me CB )) or resid 869 through 1310)) selection = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 241 or (resi \ d 242 through 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 280 or (resid 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 676 or resid 690 through 744 or (resid 745 and ( \ name N or name CA or name C or name O or name CB )) or resid 746 through 747 or \ (resid 748 and (name N or name CA or name C or name O or name CB )) or resid 749 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 13 \ 10)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 143 or (re \ sid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 through 1141 or (resid 1142 and (name N or name CA or \ name C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through \ 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147 thr \ ough 1310)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.730 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.074 24077 Z= 0.786 Angle : 1.814 10.392 32843 Z= 1.207 Chirality : 0.096 0.474 3848 Planarity : 0.013 0.189 4178 Dihedral : 13.668 89.725 8319 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.60 % Favored : 93.92 % Rotamer: Outliers : 1.14 % Allowed : 3.11 % Favored : 95.75 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 2928 helix: -1.28 (0.16), residues: 673 sheet: 0.47 (0.22), residues: 483 loop : -0.80 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 905 TYR 0.161 0.020 TYR C 904 PHE 0.126 0.014 PHE C 43 TRP 0.344 0.032 TRP C 886 HIS 0.014 0.003 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01348 / 0.79 (24009) covalent geometry : angle 1.79858 / 1.21 (32676) SS BOND : bond 0.01232 / 0.76 ( 37) SS BOND : angle 2.41168 / 1.53 ( 74) hydrogen bonds : bond 0.16218 / 10.45 ( 989) hydrogen bonds : angle 8.40558 / 5.93 ( 2688) link_NAG-ASN : bond 0.01298 / 0.82 ( 31) link_NAG-ASN : angle 4.53518 / 3.13 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 310 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 SER cc_start: 0.8301 (p) cc_final: 0.8080 (t) REVERT: B 271 GLN cc_start: 0.7612 (mt0) cc_final: 0.7378 (mm-40) REVERT: B 577 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6968 (ttm-80) REVERT: B 697 MET cc_start: 0.8376 (ptm) cc_final: 0.7909 (ptm) REVERT: B 750 SER cc_start: 0.8784 (t) cc_final: 0.8559 (m) REVERT: B 935 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7227 (mm-40) REVERT: B 973 ILE cc_start: 0.8456 (mt) cc_final: 0.8209 (mt) REVERT: C 239 GLN cc_start: -0.2496 (OUTLIER) cc_final: -0.2930 (pp30) REVERT: C 453 PHE cc_start: 0.8301 (p90) cc_final: 0.7931 (p90) REVERT: C 529 LYS cc_start: 0.8311 (tptp) cc_final: 0.7972 (mmmm) REVERT: C 731 MET cc_start: 0.9114 (mtp) cc_final: 0.8882 (mtm) REVERT: C 950 ASP cc_start: 0.8065 (t70) cc_final: 0.7723 (t0) REVERT: C 1135 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7960 (t0) outliers start: 29 outliers final: 10 residues processed: 332 average time/residue: 0.1742 time to fit residues: 89.5689 Evaluate side-chains 176 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 613 GLN A 824 ASN A 960 ASN A1088 HIS B 613 GLN B 777 ASN B 901 GLN B 925 ASN B 965 GLN B1005 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 211 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 965 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.197565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142547 restraints weight = 30853.278| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.40 r_work: 0.3287 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24077 Z= 0.144 Angle : 0.663 9.321 32843 Z= 0.347 Chirality : 0.047 0.213 3848 Planarity : 0.004 0.037 4178 Dihedral : 6.541 83.150 3200 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.58 % Rotamer: Outliers : 1.38 % Allowed : 6.05 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 2928 helix: 0.83 (0.20), residues: 660 sheet: 0.33 (0.19), residues: 664 loop : -0.60 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.022 0.002 TYR A1067 PHE 0.016 0.002 PHE B 201 TRP 0.028 0.002 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (24009) covalent geometry : angle 0.64539 / 0.34 (32676) SS BOND : bond 0.00333 / 0.24 ( 37) SS BOND : angle 1.50413 / 1.09 ( 74) hydrogen bonds : bond 0.04781 / 3.18 ( 989) hydrogen bonds : angle 6.54607 / 4.62 ( 2688) link_NAG-ASN : bond 0.00293 / 0.20 ( 31) link_NAG-ASN : angle 2.67667 / 1.77 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 ASP cc_start: 0.8103 (t0) cc_final: 0.7794 (m-30) REVERT: A 994 ASP cc_start: 0.7918 (t70) cc_final: 0.7717 (t70) REVERT: B 205 SER cc_start: 0.8557 (p) cc_final: 0.8273 (t) REVERT: B 271 GLN cc_start: 0.7666 (mt0) cc_final: 0.7233 (mm-40) REVERT: B 287 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.6511 (m-30) REVERT: B 750 SER cc_start: 0.8882 (t) cc_final: 0.8642 (m) REVERT: B 935 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6589 (mp-120) REVERT: B 973 ILE cc_start: 0.8552 (mt) cc_final: 0.8288 (mt) REVERT: B 1032 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7812 (m) REVERT: C 239 GLN cc_start: -0.2739 (OUTLIER) cc_final: -0.3106 (pp30) REVERT: C 374 PHE cc_start: 0.7664 (m-80) cc_final: 0.7418 (m-80) REVERT: C 375 SER cc_start: 0.8615 (m) cc_final: 0.8266 (t) REVERT: C 453 PHE cc_start: 0.8244 (p90) cc_final: 0.7651 (p90) REVERT: C 529 LYS cc_start: 0.8196 (tptp) cc_final: 0.7903 (mmmm) REVERT: C 814 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7679 (mtmm) REVERT: C 950 ASP cc_start: 0.8530 (t70) cc_final: 0.8289 (t0) outliers start: 35 outliers final: 21 residues processed: 215 average time/residue: 0.1567 time to fit residues: 54.6277 Evaluate side-chains 155 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 56 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 147 optimal weight: 0.0170 chunk 88 optimal weight: 0.7980 chunk 129 optimal weight: 40.0000 chunk 21 optimal weight: 4.9990 chunk 236 optimal weight: 50.0000 chunk 259 optimal weight: 4.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 87 ASN A 784 GLN A 804 GLN A1011 GLN A1048 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 784 GLN B 935 GLN B1005 GLN B1048 HIS B1064 HIS C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1088 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.198404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127562 restraints weight = 31176.618| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.42 r_work: 0.3271 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24077 Z= 0.236 Angle : 0.677 11.614 32843 Z= 0.350 Chirality : 0.049 0.220 3848 Planarity : 0.004 0.037 4178 Dihedral : 6.131 77.551 3195 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.48 % Allowed : 7.04 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 2928 helix: 0.78 (0.20), residues: 674 sheet: 0.29 (0.19), residues: 690 loop : -0.65 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1107 TYR 0.022 0.002 TYR C 396 PHE 0.018 0.002 PHE B 58 TRP 0.020 0.002 TRP C 886 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (24009) covalent geometry : angle 0.66345 / 0.35 (32676) SS BOND : bond 0.00533 / 0.39 ( 37) SS BOND : angle 1.47891 / 1.01 ( 74) hydrogen bonds : bond 0.05044 / 3.36 ( 989) hydrogen bonds : angle 6.35863 / 4.48 ( 2688) link_NAG-ASN : bond 0.00332 / 0.23 ( 31) link_NAG-ASN : angle 2.32265 / 1.52 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6224 (mp10) REVERT: A 808 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 994 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8089 (t70) REVERT: B 271 GLN cc_start: 0.7672 (mt0) cc_final: 0.7071 (mm-40) REVERT: B 577 ARG cc_start: 0.6919 (ttm-80) cc_final: 0.6558 (ttm-80) REVERT: B 750 SER cc_start: 0.8801 (t) cc_final: 0.8471 (m) REVERT: B 773 GLU cc_start: 0.8159 (tt0) cc_final: 0.7874 (tt0) REVERT: B 935 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: B 1094 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 44 ARG cc_start: 0.7638 (mtm180) cc_final: 0.6960 (mtt180) REVERT: C 335 LEU cc_start: 0.8231 (mt) cc_final: 0.7835 (tp) REVERT: C 375 SER cc_start: 0.8795 (m) cc_final: 0.8456 (p) REVERT: C 529 LYS cc_start: 0.8268 (tptp) cc_final: 0.7697 (mmmm) REVERT: C 950 ASP cc_start: 0.8643 (t70) cc_final: 0.8277 (t0) outliers start: 63 outliers final: 39 residues processed: 201 average time/residue: 0.1411 time to fit residues: 46.9282 Evaluate side-chains 171 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 123 optimal weight: 0.0670 chunk 183 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 274 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A1088 HIS B 926 GLN B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.200595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145109 restraints weight = 30992.072| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.23 r_work: 0.3302 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24077 Z= 0.124 Angle : 0.553 8.981 32843 Z= 0.287 Chirality : 0.045 0.199 3848 Planarity : 0.004 0.038 4178 Dihedral : 5.377 59.004 3190 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.89 % Allowed : 8.22 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 2928 helix: 1.24 (0.21), residues: 668 sheet: 0.53 (0.19), residues: 648 loop : -0.47 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.020 0.001 TYR A1067 PHE 0.014 0.001 PHE B 643 TRP 0.019 0.002 TRP A 64 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (24009) covalent geometry : angle 0.54315 / 0.28 (32676) SS BOND : bond 0.00271 / 0.20 ( 37) SS BOND : angle 1.12795 / 0.78 ( 74) hydrogen bonds : bond 0.03958 / 2.62 ( 989) hydrogen bonds : angle 5.94088 / 4.19 ( 2688) link_NAG-ASN : bond 0.00222 / 0.15 ( 31) link_NAG-ASN : angle 1.83936 / 1.23 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: A 808 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: A 935 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: A 994 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7831 (t70) REVERT: B 271 GLN cc_start: 0.7812 (mt0) cc_final: 0.7346 (mm-40) REVERT: B 577 ARG cc_start: 0.7218 (ttm-80) cc_final: 0.6978 (ttm-80) REVERT: B 820 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: B 935 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: B 979 ASP cc_start: 0.8350 (t0) cc_final: 0.8029 (t0) REVERT: C 436 TRP cc_start: 0.7735 (p90) cc_final: 0.7473 (p90) REVERT: C 452 LEU cc_start: 0.8117 (mt) cc_final: 0.7818 (mt) REVERT: C 453 PHE cc_start: 0.7918 (p90) cc_final: 0.7506 (p90) REVERT: C 529 LYS cc_start: 0.8281 (tptp) cc_final: 0.7918 (mmmm) REVERT: C 567 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7202 (mtm-85) REVERT: C 814 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7710 (mtmm) REVERT: C 886 TRP cc_start: 0.8007 (p90) cc_final: 0.7223 (p90) REVERT: C 950 ASP cc_start: 0.8637 (t70) cc_final: 0.8420 (t0) outliers start: 48 outliers final: 31 residues processed: 190 average time/residue: 0.1396 time to fit residues: 43.5424 Evaluate side-chains 170 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 204 optimal weight: 9.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140400 restraints weight = 31219.902| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.18 r_work: 0.3275 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24077 Z= 0.167 Angle : 0.580 9.584 32843 Z= 0.298 Chirality : 0.046 0.208 3848 Planarity : 0.004 0.039 4178 Dihedral : 5.303 58.868 3190 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.66 % Rotamer: Outliers : 2.32 % Allowed : 8.81 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 2928 helix: 1.28 (0.21), residues: 667 sheet: 0.51 (0.19), residues: 653 loop : -0.45 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.020 0.001 TYR A1067 PHE 0.016 0.001 PHE C 453 TRP 0.016 0.002 TRP A 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (24009) covalent geometry : angle 0.56797 / 0.29 (32676) SS BOND : bond 0.00377 / 0.26 ( 37) SS BOND : angle 1.46282 / 1.02 ( 74) hydrogen bonds : bond 0.04182 / 2.79 ( 989) hydrogen bonds : angle 5.90944 / 4.17 ( 2688) link_NAG-ASN : bond 0.00245 / 0.16 ( 31) link_NAG-ASN : angle 1.92368 / 1.25 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.6241 (mp10) REVERT: A 808 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: A 935 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 994 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7909 (t70) REVERT: B 271 GLN cc_start: 0.7731 (mt0) cc_final: 0.7329 (mm-40) REVERT: B 820 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: B 935 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: B 979 ASP cc_start: 0.8324 (t0) cc_final: 0.8000 (t0) REVERT: C 452 LEU cc_start: 0.8070 (mt) cc_final: 0.7798 (mt) REVERT: C 453 PHE cc_start: 0.7919 (p90) cc_final: 0.7509 (p90) REVERT: C 529 LYS cc_start: 0.8333 (tptp) cc_final: 0.7912 (mmmm) REVERT: C 567 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7132 (mtm-85) REVERT: C 886 TRP cc_start: 0.8104 (p90) cc_final: 0.7772 (p90) REVERT: C 984 LEU cc_start: 0.8546 (mm) cc_final: 0.8168 (mp) outliers start: 59 outliers final: 46 residues processed: 191 average time/residue: 0.1588 time to fit residues: 49.4550 Evaluate side-chains 183 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 168 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.199271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136847 restraints weight = 31316.060| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.83 r_work: 0.3295 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24077 Z= 0.135 Angle : 0.538 8.949 32843 Z= 0.278 Chirality : 0.044 0.201 3848 Planarity : 0.004 0.039 4178 Dihedral : 5.096 59.360 3190 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.48 % Allowed : 9.08 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2928 helix: 1.40 (0.21), residues: 674 sheet: 0.54 (0.19), residues: 655 loop : -0.38 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.019 0.001 TYR A1067 PHE 0.034 0.001 PHE B 65 TRP 0.016 0.001 TRP A 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (24009) covalent geometry : angle 0.52824 / 0.28 (32676) SS BOND : bond 0.00285 / 0.21 ( 37) SS BOND : angle 1.34667 / 0.93 ( 74) hydrogen bonds : bond 0.03874 / 2.57 ( 989) hydrogen bonds : angle 5.75817 / 4.06 ( 2688) link_NAG-ASN : bond 0.00222 / 0.15 ( 31) link_NAG-ASN : angle 1.70669 / 1.14 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5749 (mp10) REVERT: A 808 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: A 935 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: A 994 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7808 (t70) REVERT: A 1005 GLN cc_start: 0.8727 (mt0) cc_final: 0.8499 (mt0) REVERT: B 271 GLN cc_start: 0.7731 (mt0) cc_final: 0.7304 (mm-40) REVERT: B 935 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: B 979 ASP cc_start: 0.8162 (t0) cc_final: 0.7777 (t0) REVERT: C 44 ARG cc_start: 0.7420 (mtm180) cc_final: 0.7097 (mtt180) REVERT: C 453 PHE cc_start: 0.8127 (p90) cc_final: 0.7825 (p90) REVERT: C 529 LYS cc_start: 0.8328 (tptp) cc_final: 0.7875 (mmmm) REVERT: C 567 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6944 (mtt-85) REVERT: C 814 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7617 (mtmm) REVERT: C 886 TRP cc_start: 0.8037 (p90) cc_final: 0.7818 (p90) REVERT: C 984 LEU cc_start: 0.8480 (mm) cc_final: 0.8054 (mp) outliers start: 63 outliers final: 49 residues processed: 191 average time/residue: 0.1332 time to fit residues: 42.7617 Evaluate side-chains 183 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 125 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 137 optimal weight: 40.0000 chunk 142 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.199639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143429 restraints weight = 30992.313| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.20 r_work: 0.3296 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24077 Z= 0.115 Angle : 0.516 8.338 32843 Z= 0.267 Chirality : 0.044 0.198 3848 Planarity : 0.003 0.039 4178 Dihedral : 4.831 59.330 3189 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.04 % Allowed : 9.67 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2928 helix: 1.56 (0.21), residues: 675 sheet: 0.52 (0.19), residues: 658 loop : -0.34 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE A 168 TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (24009) covalent geometry : angle 0.50715 / 0.26 (32676) SS BOND : bond 0.00321 / 0.24 ( 37) SS BOND : angle 1.30237 / 0.88 ( 74) hydrogen bonds : bond 0.03642 / 2.41 ( 989) hydrogen bonds : angle 5.61640 / 3.96 ( 2688) link_NAG-ASN : bond 0.00210 / 0.15 ( 31) link_NAG-ASN : angle 1.57626 / 1.06 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.5829 (OUTLIER) cc_final: 0.5533 (mp10) REVERT: A 808 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: A 935 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 994 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7724 (t70) REVERT: A 1005 GLN cc_start: 0.8673 (mt0) cc_final: 0.8466 (mt0) REVERT: B 271 GLN cc_start: 0.7585 (mt0) cc_final: 0.7260 (mm-40) REVERT: B 820 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8231 (m-30) REVERT: B 935 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: B 979 ASP cc_start: 0.8215 (t0) cc_final: 0.7855 (t0) REVERT: C 335 LEU cc_start: 0.8395 (mt) cc_final: 0.7905 (tp) REVERT: C 396 TYR cc_start: 0.7388 (m-80) cc_final: 0.7018 (m-10) REVERT: C 453 PHE cc_start: 0.7989 (p90) cc_final: 0.7715 (p90) REVERT: C 529 LYS cc_start: 0.8336 (tptp) cc_final: 0.7966 (mmmm) REVERT: C 567 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7141 (mtt-85) outliers start: 52 outliers final: 36 residues processed: 173 average time/residue: 0.1418 time to fit residues: 40.9411 Evaluate side-chains 171 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 255 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 170 optimal weight: 0.0030 chunk 109 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 949 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140704 restraints weight = 31231.621| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.24 r_work: 0.3259 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24077 Z= 0.170 Angle : 0.563 9.691 32843 Z= 0.289 Chirality : 0.045 0.213 3848 Planarity : 0.004 0.038 4178 Dihedral : 4.915 59.304 3186 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 2.20 % Allowed : 9.75 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2928 helix: 1.34 (0.21), residues: 681 sheet: 0.50 (0.19), residues: 662 loop : -0.39 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.019 0.001 TYR A1067 PHE 0.016 0.001 PHE A1121 TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (24009) covalent geometry : angle 0.55214 / 0.29 (32676) SS BOND : bond 0.00317 / 0.23 ( 37) SS BOND : angle 1.39489 / 0.93 ( 74) hydrogen bonds : bond 0.04092 / 2.73 ( 989) hydrogen bonds : angle 5.74454 / 4.05 ( 2688) link_NAG-ASN : bond 0.00276 / 0.17 ( 31) link_NAG-ASN : angle 1.78052 / 1.18 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.5729 (OUTLIER) cc_final: 0.5415 (mp10) REVERT: A 808 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: A 935 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: A 994 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.8001 (t70) REVERT: B 271 GLN cc_start: 0.7677 (mt0) cc_final: 0.7298 (mm-40) REVERT: B 820 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: B 935 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: B 979 ASP cc_start: 0.8281 (t0) cc_final: 0.7881 (t0) REVERT: C 335 LEU cc_start: 0.8343 (mt) cc_final: 0.7907 (tp) REVERT: C 375 SER cc_start: 0.8821 (m) cc_final: 0.8529 (p) REVERT: C 396 TYR cc_start: 0.7421 (m-80) cc_final: 0.7026 (m-10) REVERT: C 436 TRP cc_start: 0.7583 (p90) cc_final: 0.7207 (p90) REVERT: C 529 LYS cc_start: 0.8365 (tptp) cc_final: 0.7944 (mmmm) REVERT: C 567 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7040 (mtt-85) outliers start: 56 outliers final: 38 residues processed: 180 average time/residue: 0.1427 time to fit residues: 42.6138 Evaluate side-chains 173 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 252 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 114 optimal weight: 0.0870 chunk 179 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.195722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140433 restraints weight = 30674.406| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.29 r_work: 0.3263 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24077 Z= 0.125 Angle : 0.522 9.051 32843 Z= 0.269 Chirality : 0.044 0.201 3848 Planarity : 0.003 0.038 4178 Dihedral : 4.741 59.006 3184 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 1.85 % Allowed : 10.10 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2928 helix: 1.50 (0.21), residues: 682 sheet: 0.50 (0.19), residues: 656 loop : -0.40 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.018 0.001 TYR A1067 PHE 0.031 0.001 PHE C 453 TRP 0.015 0.001 TRP A 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24009) covalent geometry : angle 0.51165 / 0.27 (32676) SS BOND : bond 0.00277 / 0.21 ( 37) SS BOND : angle 1.28006 / 0.86 ( 74) hydrogen bonds : bond 0.03704 / 2.46 ( 989) hydrogen bonds : angle 5.61583 / 3.96 ( 2688) link_NAG-ASN : bond 0.00369 / 0.17 ( 31) link_NAG-ASN : angle 1.72151 / 1.14 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5358 (mp10) REVERT: A 808 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: A 935 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: A 994 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7854 (t70) REVERT: B 271 GLN cc_start: 0.7604 (mt0) cc_final: 0.7243 (mm-40) REVERT: B 820 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8353 (m-30) REVERT: B 935 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6547 (mp10) REVERT: B 979 ASP cc_start: 0.8231 (t0) cc_final: 0.7850 (t0) REVERT: C 375 SER cc_start: 0.8787 (m) cc_final: 0.8499 (p) REVERT: C 396 TYR cc_start: 0.7542 (m-80) cc_final: 0.7157 (m-10) REVERT: C 436 TRP cc_start: 0.7503 (p90) cc_final: 0.7198 (p90) REVERT: C 453 PHE cc_start: 0.7706 (p90) cc_final: 0.7331 (p90) REVERT: C 529 LYS cc_start: 0.8352 (tptp) cc_final: 0.7915 (mmmm) REVERT: C 567 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7037 (mtt-85) outliers start: 47 outliers final: 39 residues processed: 169 average time/residue: 0.1365 time to fit residues: 38.3123 Evaluate side-chains 173 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 118 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 189 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 251 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.196043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139218 restraints weight = 30758.124| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.23 r_work: 0.3273 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24077 Z= 0.113 Angle : 0.508 8.118 32843 Z= 0.263 Chirality : 0.044 0.245 3848 Planarity : 0.003 0.038 4178 Dihedral : 4.613 58.011 3184 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.81 % Allowed : 10.14 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2928 helix: 1.56 (0.21), residues: 682 sheet: 0.51 (0.19), residues: 669 loop : -0.35 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.019 0.001 TYR C1067 PHE 0.030 0.001 PHE C 453 TRP 0.016 0.001 TRP A 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (24009) covalent geometry : angle 0.49701 / 0.26 (32676) SS BOND : bond 0.00234 / 0.17 ( 37) SS BOND : angle 1.46362 / 0.93 ( 74) hydrogen bonds : bond 0.03525 / 2.33 ( 989) hydrogen bonds : angle 5.51719 / 3.88 ( 2688) link_NAG-ASN : bond 0.00313 / 0.16 ( 31) link_NAG-ASN : angle 1.64004 / 1.08 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.5575 (OUTLIER) cc_final: 0.5257 (mp10) REVERT: A 808 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: A 935 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 994 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7840 (t70) REVERT: B 271 GLN cc_start: 0.7597 (mt0) cc_final: 0.7232 (mm-40) REVERT: B 820 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: B 935 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: B 979 ASP cc_start: 0.8250 (t70) cc_final: 0.7874 (t0) REVERT: C 375 SER cc_start: 0.8838 (m) cc_final: 0.8567 (p) REVERT: C 396 TYR cc_start: 0.7529 (m-80) cc_final: 0.7121 (m-10) REVERT: C 453 PHE cc_start: 0.7730 (p90) cc_final: 0.7368 (p90) REVERT: C 529 LYS cc_start: 0.8388 (tptp) cc_final: 0.8001 (mmmm) REVERT: C 567 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7051 (mtt-85) outliers start: 46 outliers final: 34 residues processed: 171 average time/residue: 0.1411 time to fit residues: 40.2319 Evaluate side-chains 166 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 142 optimal weight: 6.9990 chunk 230 optimal weight: 0.0170 chunk 161 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.194174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142549 restraints weight = 30671.374| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.36 r_work: 0.3281 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24077 Z= 0.188 Angle : 0.571 10.139 32843 Z= 0.293 Chirality : 0.046 0.221 3848 Planarity : 0.004 0.038 4178 Dihedral : 4.819 58.498 3184 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 1.69 % Allowed : 10.42 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 2928 helix: 1.31 (0.21), residues: 681 sheet: 0.48 (0.19), residues: 672 loop : -0.42 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.018 0.001 TYR A1067 PHE 0.030 0.002 PHE C 453 TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (24009) covalent geometry : angle 0.55864 / 0.29 (32676) SS BOND : bond 0.00309 / 0.22 ( 37) SS BOND : angle 1.74646 / 1.10 ( 74) hydrogen bonds : bond 0.04123 / 2.75 ( 989) hydrogen bonds : angle 5.73594 / 4.04 ( 2688) link_NAG-ASN : bond 0.00280 / 0.17 ( 31) link_NAG-ASN : angle 1.78687 / 1.18 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7158.11 seconds wall clock time: 122 minutes 47.34 seconds (7367.34 seconds total)